Msgn1 (mesogenin 1) - Rat Genome Database

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Gene: Msgn1 (mesogenin 1) Rattus norvegicus
Analyze
Symbol: Msgn1
Name: mesogenin 1
RGD ID: 1587516
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in mesoderm formation and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within segment specification and somitogenesis. Predicted to be active in nucleus. Orthologous to human MSGN1 (mesogenin 1); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 6-propyl-2-thiouracil; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC689864; mesogenin-1; similar to mesogenin 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8639,631,868 - 39,632,508 (-)NCBIGRCr8
mRatBN7.2633,912,787 - 33,913,427 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl633,912,787 - 33,913,427 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx634,212,134 - 34,212,774 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0634,528,073 - 34,528,713 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0633,999,060 - 33,999,700 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0636,876,165 - 36,876,805 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl636,876,165 - 36,876,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0646,626,278 - 46,626,918 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4634,642,722 - 34,643,362 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera633,319,681 - 33,320,321 (-)NCBICelera
Cytogenetic Map6q15NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11124811   PMID:21750544  


Genomics

Comparative Map Data
Msgn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8639,631,868 - 39,632,508 (-)NCBIGRCr8
mRatBN7.2633,912,787 - 33,913,427 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl633,912,787 - 33,913,427 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx634,212,134 - 34,212,774 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0634,528,073 - 34,528,713 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0633,999,060 - 33,999,700 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0636,876,165 - 36,876,805 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl636,876,165 - 36,876,805 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0646,626,278 - 46,626,918 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4634,642,722 - 34,643,362 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera633,319,681 - 33,320,321 (-)NCBICelera
Cytogenetic Map6q15NCBI
MSGN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38217,816,460 - 17,817,798 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl217,816,460 - 17,817,798 (+)EnsemblGRCh38hg38GRCh38
GRCh37217,997,727 - 17,999,065 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36217,861,267 - 17,861,848 (+)NCBINCBI36Build 36hg18NCBI36
Celera217,878,053 - 17,878,634 (+)NCBICelera
Cytogenetic Map2p24.2NCBI
HuRef217,772,843 - 17,773,424 (+)NCBIHuRef
CHM1_1217,927,062 - 17,927,643 (+)NCBICHM1_1
T2T-CHM13v2.0217,848,194 - 17,849,532 (+)NCBIT2T-CHM13v2.0
Msgn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391211,258,383 - 11,258,949 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1211,258,361 - 11,258,973 (-)EnsemblGRCm39 Ensembl
GRCm381211,208,382 - 11,208,948 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1211,208,360 - 11,208,972 (-)EnsemblGRCm38mm10GRCm38
MGSCv371211,215,188 - 11,215,754 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361211,234,725 - 11,235,291 (-)NCBIMGSCv36mm8
Celera1211,552,514 - 11,553,080 (-)NCBICelera
Cytogenetic Map12A1.1NCBI
cM Map125.58NCBI
Msgn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955469617,029 - 617,610 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955469617,029 - 617,610 (+)NCBIChiLan1.0ChiLan1.0
MSGN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212108,710,407 - 108,712,710 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A108,714,373 - 108,716,676 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A17,797,769 - 17,799,243 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A17,926,024 - 17,927,301 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A17,926,027 - 17,926,608 (+)Ensemblpanpan1.1panPan2
MSGN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11713,266,674 - 13,267,968 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1713,266,674 - 13,267,240 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1713,218,674 - 13,219,870 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01713,403,492 - 13,404,688 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1713,403,492 - 13,404,058 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11713,261,563 - 13,262,765 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01713,272,831 - 13,274,030 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01713,299,019 - 13,300,215 (+)NCBIUU_Cfam_GSD_1.0
Msgn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629257,694,963 - 57,710,008 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649313,129,883 - 13,130,464 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649313,129,883 - 13,130,464 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSGN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3120,034,043 - 120,034,624 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13120,033,980 - 120,034,624 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23128,181,840 - 128,182,492 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MSGN1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11489,852,082 - 89,855,540 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1489,853,400 - 89,853,981 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604522,359,570 - 22,361,544 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Msgn1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624738756,679 - 757,258 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624738756,679 - 757,278 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:80
Interacting mature miRNAs:86
Transcripts:ENSRNOT00000006482
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat

Markers in Region
RH141807  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2633,912,629 - 33,912,826 (+)MAPPERmRatBN7.2
Rnor_6.0636,876,008 - 36,876,204NCBIRnor6.0
Rnor_5.0646,626,121 - 46,626,317UniSTSRnor5.0
RGSC_v3.4634,642,565 - 34,642,761UniSTSRGSC3.4
Celera633,319,524 - 33,319,720UniSTS
RH 3.4 Map6124.11UniSTS
Cytogenetic Map6q14UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium
Low
Below cutoff 2 2 1 2 2 2 12 12 2 2

Sequence


RefSeq Acc Id: ENSRNOT00000006482   ⟹   ENSRNOP00000006482
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl633,912,787 - 33,913,427 (-)Ensembl
Rnor_6.0 Ensembl636,876,165 - 36,876,805 (-)Ensembl
RefSeq Acc Id: NM_001109551   ⟹   NP_001103021
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8639,631,868 - 39,632,508 (-)NCBI
mRatBN7.2633,912,787 - 33,913,427 (-)NCBI
Rnor_6.0636,876,165 - 36,876,805 (-)NCBI
Rnor_5.0646,626,278 - 46,626,918 (-)NCBI
RGSC_v3.4634,642,722 - 34,643,362 (-)RGD
Celera633,319,681 - 33,320,321 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103021 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03098 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006482
  ENSRNOP00000006482.1
RefSeq Acc Id: NP_001103021   ⟸   NM_001109551
- UniProtKB: D3ZVR2 (UniProtKB/TrEMBL),   A6HAP3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006482   ⟸   ENSRNOT00000006482
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZVR2-F1-model_v2 AlphaFold D3ZVR2 1-187 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1587516 AgrOrtholog
BioCyc Gene G2FUF-38147 BioCyc
Ensembl Genes ENSRNOG00000028518 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006482 ENTREZGENE
  ENSRNOT00000006482.4 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
  Mesogenin/MesP UniProtKB/TrEMBL
KEGG Report rno:689864 UniProtKB/TrEMBL
NCBI Gene 689864 ENTREZGENE
PANTHER MESOGENIN-1 UniProtKB/TrEMBL
  PTHR20937 UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
PhenoGen Msgn1 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028518 RatGTEx
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt A6HAP3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZVR2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-06 Msgn1  mesogenin 1  LOC689864  similar to mesogenin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC689864  similar to mesogenin 1  LOC686162  similar to mesogenin 1  Data merged from RGD:1585438 1643240 APPROVED
2006-11-19 LOC689864  similar to mesogenin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC686162  similar to mesogenin 1      Symbol and Name status set to provisional 70820 PROVISIONAL